Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.

The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to perform this function, one of the proteins, the F-box, is responsible for binding to the substrate, thereby allowing a different protein in the complex, the ubiquitin-conjugating enzyme, to access the substrate and attach ubiquitin. The F-box protein has multiple interchangeable variants so that the complex can recognize different substrates. Additionally, different organisms can have different sets of F-box protein variants. Humans have 38 known variants, Saccharomyces cerevisiae has 11, Drosophila has 22, and C. elegans has 326.  This variation enables the complex to target a large spectrum of proteins by changing just one of its components.

These interchangeable variants are often an outcome of gene duplication. During molecular evolution, the gene for a beneficial protein can sometimes duplicate during DNA replication due to reasons, such as ectopic recombination, replication slippage, aneuploidy, polyploidy, and retrotransposition.  This duplicated copy of the gene can further undergo mutations while being transferred from one generation to the next as the mutation does not affect the function of the original gene.  These mutations result in variants of a gene that are responsible for proteins, like the F-box, which are functionally similar but have different substrate specificities.